Multiple sequence alignment - TraesCS1A01G400600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1A01G400600 chr1A 100.000 2957 0 0 1 2957 564397849 564394893 0.000000e+00 5461.0
1 TraesCS1A01G400600 chr1D 90.567 2152 129 29 100 2207 470734418 470732297 0.000000e+00 2782.0
2 TraesCS1A01G400600 chr1D 91.589 749 41 9 2197 2924 470732182 470731435 0.000000e+00 1014.0
3 TraesCS1A01G400600 chr1D 93.069 101 2 2 4 100 470734557 470734458 3.070000e-30 143.0
4 TraesCS1A01G400600 chr1B 89.617 2013 117 45 109 2071 654032176 654030206 0.000000e+00 2475.0
5 TraesCS1A01G400600 chr1B 90.652 460 35 5 2215 2666 654030037 654029578 3.260000e-169 604.0
6 TraesCS1A01G400600 chr1B 91.005 189 12 3 2740 2924 654029583 654029396 1.760000e-62 250.0
7 TraesCS1A01G400600 chr2D 86.603 948 112 12 1027 1965 25024781 25025722 0.000000e+00 1033.0
8 TraesCS1A01G400600 chr2A 83.824 952 101 20 1027 1965 27499916 27500827 0.000000e+00 856.0
9 TraesCS1A01G400600 chr2A 89.202 213 21 2 2719 2930 83249848 83250059 6.280000e-67 265.0
10 TraesCS1A01G400600 chr3B 89.671 213 20 2 2719 2930 16303250 16303039 1.350000e-68 270.0
11 TraesCS1A01G400600 chr3B 79.062 320 39 18 2641 2957 763531066 763530772 8.360000e-46 195.0
12 TraesCS1A01G400600 chr7B 91.667 132 9 2 2800 2930 176807247 176807117 6.510000e-42 182.0
13 TraesCS1A01G400600 chrUn 92.727 55 4 0 2641 2695 287140624 287140570 2.440000e-11 80.5
14 TraesCS1A01G400600 chrUn 92.727 55 4 0 2641 2695 287146792 287146738 2.440000e-11 80.5
15 TraesCS1A01G400600 chrUn 91.379 58 5 0 2638 2695 293606170 293606227 2.440000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G400600 chr1A 564394893 564397849 2956 True 5461.000000 5461 100.000000 1 2957 1 chr1A.!!$R1 2956
1 TraesCS1A01G400600 chr1D 470731435 470734557 3122 True 1313.000000 2782 91.741667 4 2924 3 chr1D.!!$R1 2920
2 TraesCS1A01G400600 chr1B 654029396 654032176 2780 True 1109.666667 2475 90.424667 109 2924 3 chr1B.!!$R1 2815
3 TraesCS1A01G400600 chr2D 25024781 25025722 941 False 1033.000000 1033 86.603000 1027 1965 1 chr2D.!!$F1 938
4 TraesCS1A01G400600 chr2A 27499916 27500827 911 False 856.000000 856 83.824000 1027 1965 1 chr2A.!!$F1 938

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
874 950 0.474184 GGGGATGAACGGATGATGGT 59.526 55.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 2508 0.604578 TGCAAATTGCTCCTTGGCTC 59.395 50.0 19.34 0.0 45.31 4.7 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 105 2.732094 ACCGCTCGAAAACGACCG 60.732 61.111 3.94 0.00 0.00 4.79
101 106 2.429571 CCGCTCGAAAACGACCGA 60.430 61.111 8.51 0.00 0.00 4.69
223 268 0.605589 CCCACCCAAAAGACTCGTCC 60.606 60.000 0.00 0.00 0.00 4.79
686 749 2.261430 CTGCCACATCTAGCCTGCCA 62.261 60.000 0.00 0.00 0.00 4.92
707 774 4.384098 CCACCAGCCATGTATTCTCTGTTA 60.384 45.833 0.00 0.00 0.00 2.41
708 775 4.813161 CACCAGCCATGTATTCTCTGTTAG 59.187 45.833 0.00 0.00 0.00 2.34
709 776 4.471386 ACCAGCCATGTATTCTCTGTTAGT 59.529 41.667 0.00 0.00 0.00 2.24
710 777 5.661312 ACCAGCCATGTATTCTCTGTTAGTA 59.339 40.000 0.00 0.00 0.00 1.82
711 778 5.986135 CCAGCCATGTATTCTCTGTTAGTAC 59.014 44.000 0.00 0.00 0.00 2.73
712 779 6.183360 CCAGCCATGTATTCTCTGTTAGTACT 60.183 42.308 0.00 0.00 0.00 2.73
779 854 5.521372 TCGTTTTGATCGATCGACTACTCTA 59.479 40.000 22.06 8.21 32.30 2.43
780 855 5.616383 CGTTTTGATCGATCGACTACTCTAC 59.384 44.000 22.06 11.47 0.00 2.59
781 856 6.509837 CGTTTTGATCGATCGACTACTCTACT 60.510 42.308 22.06 0.00 0.00 2.57
782 857 6.528014 TTTGATCGATCGACTACTCTACTC 57.472 41.667 22.06 11.14 0.00 2.59
783 858 5.456548 TGATCGATCGACTACTCTACTCT 57.543 43.478 22.06 0.00 0.00 3.24
805 880 3.823873 TGCTGTAAATTTTCCACCGTGAT 59.176 39.130 0.00 0.00 0.00 3.06
839 914 5.737860 GGAAAAATTCCCAATCTGCTCAAT 58.262 37.500 0.00 0.00 44.30 2.57
847 922 7.664552 TTCCCAATCTGCTCAATATGATTTT 57.335 32.000 0.00 0.00 0.00 1.82
849 924 6.266103 TCCCAATCTGCTCAATATGATTTTCC 59.734 38.462 0.00 0.00 0.00 3.13
855 930 6.037500 TCTGCTCAATATGATTTTCCTCGTTG 59.962 38.462 0.00 0.00 0.00 4.10
874 950 0.474184 GGGGATGAACGGATGATGGT 59.526 55.000 0.00 0.00 0.00 3.55
875 951 1.597742 GGGATGAACGGATGATGGTG 58.402 55.000 0.00 0.00 0.00 4.17
876 952 1.134098 GGGATGAACGGATGATGGTGT 60.134 52.381 0.00 0.00 0.00 4.16
878 954 2.419990 GGATGAACGGATGATGGTGTGA 60.420 50.000 0.00 0.00 0.00 3.58
879 955 2.849294 TGAACGGATGATGGTGTGAA 57.151 45.000 0.00 0.00 0.00 3.18
880 956 3.348647 TGAACGGATGATGGTGTGAAT 57.651 42.857 0.00 0.00 0.00 2.57
958 1075 1.006337 TCGTGCAAATGCTTTGGGC 60.006 52.632 6.97 6.55 40.94 5.36
988 1105 0.545309 TGGGAGTGAAGGAGGACTGG 60.545 60.000 0.00 0.00 0.00 4.00
1020 1137 4.899239 GCCATGGAGGAGGCGACG 62.899 72.222 18.40 0.00 41.70 5.12
1353 1476 2.807045 GTGGACTGCACGAGCTCG 60.807 66.667 33.45 33.45 46.33 5.03
1548 1671 3.087253 CCGACCTACATGGGCCCA 61.087 66.667 30.92 30.92 42.31 5.36
1719 1842 1.154205 GCGTGATGGACATCTTCGGG 61.154 60.000 21.29 7.76 38.60 5.14
1755 1887 2.362120 GACTTCTCGTCCGGGGGA 60.362 66.667 0.00 0.00 36.62 4.81
1965 2100 1.234615 TGCGCAAGTAAGGCAAGACC 61.235 55.000 8.16 0.00 41.68 3.85
1969 2104 1.234821 CAAGTAAGGCAAGACCGCAA 58.765 50.000 0.00 0.00 46.52 4.85
2022 2157 6.533012 CGGATATGAATCTCATGGTCATGTAC 59.467 42.308 10.32 5.82 37.70 2.90
2056 2193 7.493971 AGTTCAGACAAAATTCGATCTCTATGG 59.506 37.037 0.00 0.00 0.00 2.74
2060 2197 6.204301 AGACAAAATTCGATCTCTATGGCATG 59.796 38.462 10.98 0.16 0.00 4.06
2073 2210 6.208402 TCTCTATGGCATGTTTTTAAGCAACA 59.792 34.615 10.98 5.12 38.49 3.33
2077 2214 6.297694 TGGCATGTTTTTAAGCAACAATTC 57.702 33.333 6.43 1.72 37.67 2.17
2080 2217 6.418141 GCATGTTTTTAAGCAACAATTCGTT 58.582 32.000 6.43 0.00 37.67 3.85
2083 2220 9.352163 CATGTTTTTAAGCAACAATTCGTTAAC 57.648 29.630 6.43 0.00 37.67 2.01
2084 2221 7.896894 TGTTTTTAAGCAACAATTCGTTAACC 58.103 30.769 0.00 0.00 35.52 2.85
2085 2222 7.760340 TGTTTTTAAGCAACAATTCGTTAACCT 59.240 29.630 0.00 0.00 35.52 3.50
2092 2229 7.250569 AGCAACAATTCGTTAACCTTATCATG 58.749 34.615 0.00 0.00 35.52 3.07
2096 2233 7.930217 ACAATTCGTTAACCTTATCATGGATG 58.070 34.615 0.00 0.00 0.00 3.51
2115 2269 7.566760 TGGATGATAATGTTATCGTGCTTTT 57.433 32.000 20.09 0.00 43.63 2.27
2134 2288 2.768253 TCTCGCTGATTTGTGGATGT 57.232 45.000 0.00 0.00 0.00 3.06
2139 2293 5.647658 TCTCGCTGATTTGTGGATGTTATTT 59.352 36.000 0.00 0.00 0.00 1.40
2143 2297 6.536688 GCTGATTTGTGGATGTTATTTTTGC 58.463 36.000 0.00 0.00 0.00 3.68
2145 2299 7.622672 GCTGATTTGTGGATGTTATTTTTGCTG 60.623 37.037 0.00 0.00 0.00 4.41
2146 2300 5.921004 TTTGTGGATGTTATTTTTGCTGC 57.079 34.783 0.00 0.00 0.00 5.25
2149 2303 5.229423 TGTGGATGTTATTTTTGCTGCTTC 58.771 37.500 0.00 0.00 0.00 3.86
2150 2304 4.627035 GTGGATGTTATTTTTGCTGCTTCC 59.373 41.667 0.00 0.00 0.00 3.46
2152 2306 5.011943 TGGATGTTATTTTTGCTGCTTCCTT 59.988 36.000 0.00 0.00 0.00 3.36
2153 2307 5.578336 GGATGTTATTTTTGCTGCTTCCTTC 59.422 40.000 0.00 0.00 0.00 3.46
2155 2309 6.160576 TGTTATTTTTGCTGCTTCCTTCTT 57.839 33.333 0.00 0.00 0.00 2.52
2156 2310 5.984926 TGTTATTTTTGCTGCTTCCTTCTTG 59.015 36.000 0.00 0.00 0.00 3.02
2157 2311 4.942761 ATTTTTGCTGCTTCCTTCTTGA 57.057 36.364 0.00 0.00 0.00 3.02
2158 2312 4.942761 TTTTTGCTGCTTCCTTCTTGAT 57.057 36.364 0.00 0.00 0.00 2.57
2159 2313 3.928727 TTTGCTGCTTCCTTCTTGATG 57.071 42.857 0.00 0.00 0.00 3.07
2160 2314 2.574006 TGCTGCTTCCTTCTTGATGT 57.426 45.000 0.00 0.00 0.00 3.06
2162 2316 4.019792 TGCTGCTTCCTTCTTGATGTAA 57.980 40.909 0.00 0.00 0.00 2.41
2164 2318 3.753272 GCTGCTTCCTTCTTGATGTAACA 59.247 43.478 0.00 0.00 0.00 2.41
2165 2319 4.397417 GCTGCTTCCTTCTTGATGTAACAT 59.603 41.667 0.00 0.00 0.00 2.71
2166 2320 5.105997 GCTGCTTCCTTCTTGATGTAACATT 60.106 40.000 0.00 0.00 0.00 2.71
2170 2324 7.119699 TGCTTCCTTCTTGATGTAACATTAGTG 59.880 37.037 0.00 0.00 0.00 2.74
2171 2325 7.414540 GCTTCCTTCTTGATGTAACATTAGTGG 60.415 40.741 0.00 0.00 0.00 4.00
2179 2333 9.214957 CTTGATGTAACATTAGTGGTTCAGTTA 57.785 33.333 0.00 0.00 0.00 2.24
2193 2347 5.105146 TGGTTCAGTTATTTTTGCCAAGTGT 60.105 36.000 0.00 0.00 0.00 3.55
2210 2364 7.430992 CCAAGTGTGGTATTCAGATGATATG 57.569 40.000 0.00 0.00 40.42 1.78
2213 2495 7.855784 AGTGTGGTATTCAGATGATATGGTA 57.144 36.000 0.00 0.00 0.00 3.25
2217 2499 9.025041 TGTGGTATTCAGATGATATGGTAGTAG 57.975 37.037 0.00 0.00 0.00 2.57
2331 2628 6.278172 TGCAAGATAGCATATCTACTCTGG 57.722 41.667 0.00 0.00 40.11 3.86
2334 2631 6.563422 CAAGATAGCATATCTACTCTGGAGC 58.437 44.000 0.00 0.00 0.00 4.70
2335 2632 5.200483 AGATAGCATATCTACTCTGGAGCC 58.800 45.833 0.00 0.00 0.00 4.70
2336 2633 3.541242 AGCATATCTACTCTGGAGCCT 57.459 47.619 0.00 0.00 0.00 4.58
2338 2635 2.495669 GCATATCTACTCTGGAGCCTCC 59.504 54.545 2.98 2.98 36.96 4.30
2384 2684 4.959210 TCTCCTTATCTCTTTCACTCCCAG 59.041 45.833 0.00 0.00 0.00 4.45
2401 2703 1.000938 CCAGAAACCTTCAGCAGCAAC 60.001 52.381 0.00 0.00 0.00 4.17
2604 2909 3.130340 GGTCTCACTCTCTCCATCTTGAC 59.870 52.174 0.00 0.00 0.00 3.18
2671 2976 8.624776 TCTGATGATAGATGTAGTAGTGTGTTG 58.375 37.037 0.00 0.00 0.00 3.33
2697 3002 6.384258 TCTGTCACTAGTTCTGATAGATGC 57.616 41.667 0.00 0.00 32.65 3.91
2728 3033 2.121948 TCCCTTCAGACTGGATGGATG 58.878 52.381 3.70 0.00 34.82 3.51
2738 3043 0.034186 TGGATGGATGGTGCAAGTCC 60.034 55.000 6.38 6.38 0.00 3.85
2805 3114 8.139350 TCATTGCTTTGATATGATGGAATGTTC 58.861 33.333 0.00 0.00 37.59 3.18
2820 3129 1.649321 TGTTCCTGCTGGACTCTGAT 58.351 50.000 12.53 0.00 43.06 2.90
2917 3226 1.038681 TCACGGCTGCGGATAAGGTA 61.039 55.000 14.45 0.00 0.00 3.08
2918 3227 0.597637 CACGGCTGCGGATAAGGTAG 60.598 60.000 14.45 0.00 0.00 3.18
2919 3228 1.041447 ACGGCTGCGGATAAGGTAGT 61.041 55.000 14.45 0.00 0.00 2.73
2921 3230 0.880718 GGCTGCGGATAAGGTAGTGC 60.881 60.000 0.00 0.00 0.00 4.40
2922 3231 0.179084 GCTGCGGATAAGGTAGTGCA 60.179 55.000 0.00 0.00 0.00 4.57
2923 3232 1.541233 GCTGCGGATAAGGTAGTGCAT 60.541 52.381 0.00 0.00 0.00 3.96
2924 3233 2.838736 CTGCGGATAAGGTAGTGCATT 58.161 47.619 0.00 0.00 0.00 3.56
2925 3234 3.206150 CTGCGGATAAGGTAGTGCATTT 58.794 45.455 0.00 0.00 0.00 2.32
2926 3235 4.377021 CTGCGGATAAGGTAGTGCATTTA 58.623 43.478 0.00 0.00 0.00 1.40
2927 3236 4.968259 TGCGGATAAGGTAGTGCATTTAT 58.032 39.130 0.00 0.00 0.00 1.40
2928 3237 5.373222 TGCGGATAAGGTAGTGCATTTATT 58.627 37.500 0.00 0.00 0.00 1.40
2929 3238 5.825679 TGCGGATAAGGTAGTGCATTTATTT 59.174 36.000 0.00 0.00 0.00 1.40
2930 3239 6.320164 TGCGGATAAGGTAGTGCATTTATTTT 59.680 34.615 0.00 0.00 0.00 1.82
2931 3240 6.856426 GCGGATAAGGTAGTGCATTTATTTTC 59.144 38.462 0.00 0.00 0.00 2.29
2932 3241 7.360361 CGGATAAGGTAGTGCATTTATTTTCC 58.640 38.462 0.00 0.00 0.00 3.13
2933 3242 7.012894 CGGATAAGGTAGTGCATTTATTTTCCA 59.987 37.037 0.00 0.00 0.00 3.53
2934 3243 8.860088 GGATAAGGTAGTGCATTTATTTTCCAT 58.140 33.333 0.00 0.00 0.00 3.41
2935 3244 9.683069 GATAAGGTAGTGCATTTATTTTCCATG 57.317 33.333 0.00 0.00 0.00 3.66
2936 3245 5.906073 AGGTAGTGCATTTATTTTCCATGC 58.094 37.500 0.00 0.00 43.13 4.06
2937 3246 5.658190 AGGTAGTGCATTTATTTTCCATGCT 59.342 36.000 5.07 0.00 43.22 3.79
2938 3247 5.979517 GGTAGTGCATTTATTTTCCATGCTC 59.020 40.000 5.07 1.74 43.22 4.26
2939 3248 5.927281 AGTGCATTTATTTTCCATGCTCT 57.073 34.783 5.07 3.92 43.22 4.09
2940 3249 5.657474 AGTGCATTTATTTTCCATGCTCTG 58.343 37.500 7.05 0.00 42.98 3.35
2941 3250 5.186409 AGTGCATTTATTTTCCATGCTCTGT 59.814 36.000 7.05 0.00 42.98 3.41
2942 3251 5.870978 GTGCATTTATTTTCCATGCTCTGTT 59.129 36.000 5.07 0.00 43.22 3.16
2943 3252 6.369615 GTGCATTTATTTTCCATGCTCTGTTT 59.630 34.615 5.07 0.00 43.22 2.83
2944 3253 6.935771 TGCATTTATTTTCCATGCTCTGTTTT 59.064 30.769 5.07 0.00 43.22 2.43
2945 3254 7.444792 TGCATTTATTTTCCATGCTCTGTTTTT 59.555 29.630 5.07 0.00 43.22 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.512942 TTCAGAAAAGGTGATCCATGGTA 57.487 39.130 12.58 0.00 35.89 3.25
1 2 4.387026 TTCAGAAAAGGTGATCCATGGT 57.613 40.909 12.58 0.00 35.89 3.55
2 3 5.477984 TCTTTTCAGAAAAGGTGATCCATGG 59.522 40.000 28.05 4.97 46.11 3.66
74 79 2.757155 TTTCGAGCGGTGCATCACGA 62.757 55.000 11.74 9.22 34.83 4.35
100 105 2.747855 CCGGCTTGACTTGGCCTC 60.748 66.667 3.32 0.00 45.57 4.70
101 106 4.351054 CCCGGCTTGACTTGGCCT 62.351 66.667 3.32 0.00 45.57 5.19
223 268 0.321671 TCTTGGAAAGTCGGGAGCTG 59.678 55.000 0.00 0.00 46.34 4.24
686 749 4.471386 ACTAACAGAGAATACATGGCTGGT 59.529 41.667 0.00 0.00 0.00 4.00
707 774 7.052142 AGAGCAACTAACAAACAGTAGTACT 57.948 36.000 0.00 0.00 0.00 2.73
708 775 6.087820 CGAGAGCAACTAACAAACAGTAGTAC 59.912 42.308 0.00 0.00 0.00 2.73
709 776 6.147581 CGAGAGCAACTAACAAACAGTAGTA 58.852 40.000 0.00 0.00 0.00 1.82
710 777 4.982916 CGAGAGCAACTAACAAACAGTAGT 59.017 41.667 0.00 0.00 0.00 2.73
711 778 4.386049 CCGAGAGCAACTAACAAACAGTAG 59.614 45.833 0.00 0.00 0.00 2.57
712 779 4.202182 ACCGAGAGCAACTAACAAACAGTA 60.202 41.667 0.00 0.00 0.00 2.74
779 854 3.502211 CGGTGGAAAATTTACAGCAGAGT 59.498 43.478 18.71 0.00 33.18 3.24
780 855 3.502211 ACGGTGGAAAATTTACAGCAGAG 59.498 43.478 18.71 6.48 33.18 3.35
781 856 3.252215 CACGGTGGAAAATTTACAGCAGA 59.748 43.478 18.71 0.00 33.18 4.26
782 857 3.252215 TCACGGTGGAAAATTTACAGCAG 59.748 43.478 18.71 13.54 33.18 4.24
783 858 3.215151 TCACGGTGGAAAATTTACAGCA 58.785 40.909 18.71 0.00 33.18 4.41
839 914 4.165180 TCATCCCCAACGAGGAAAATCATA 59.835 41.667 0.00 0.00 41.22 2.15
855 930 0.474184 ACCATCATCCGTTCATCCCC 59.526 55.000 0.00 0.00 0.00 4.81
880 956 8.881743 GCTCCATAAATTAAAATTGCATCACAA 58.118 29.630 0.00 0.00 44.01 3.33
900 988 0.988832 TAAACAACTCCCGGCTCCAT 59.011 50.000 0.00 0.00 0.00 3.41
958 1075 2.566833 TCACTCCCAATCACCAACTG 57.433 50.000 0.00 0.00 0.00 3.16
965 1082 1.909302 GTCCTCCTTCACTCCCAATCA 59.091 52.381 0.00 0.00 0.00 2.57
988 1105 2.295885 CATGGCCATGACCTCTTCTTC 58.704 52.381 37.84 0.00 41.20 2.87
1074 1197 4.592192 ACGCCGATGCCGATCCAG 62.592 66.667 0.00 0.00 38.22 3.86
1755 1887 0.750249 TGATGATGTACCGCACGGAT 59.250 50.000 17.40 0.00 38.96 4.18
1944 2079 1.200020 GTCTTGCCTTACTTGCGCATT 59.800 47.619 12.75 3.63 31.44 3.56
1945 2080 0.804989 GTCTTGCCTTACTTGCGCAT 59.195 50.000 12.75 0.00 31.44 4.73
1946 2081 1.234615 GGTCTTGCCTTACTTGCGCA 61.235 55.000 5.66 5.66 0.00 6.09
1947 2082 1.502190 GGTCTTGCCTTACTTGCGC 59.498 57.895 0.00 0.00 0.00 6.09
1948 2083 1.787847 CGGTCTTGCCTTACTTGCG 59.212 57.895 0.00 0.00 34.25 4.85
1949 2084 1.234615 TGCGGTCTTGCCTTACTTGC 61.235 55.000 0.00 0.00 34.25 4.01
1965 2100 2.954753 GACGAACACCTGCCTTGCG 61.955 63.158 0.00 0.00 0.00 4.85
1969 2104 1.608590 CATTTTGACGAACACCTGCCT 59.391 47.619 0.00 0.00 0.00 4.75
2030 2165 7.493971 CCATAGAGATCGAATTTTGTCTGAACT 59.506 37.037 0.00 0.00 0.00 3.01
2031 2166 7.625553 CCATAGAGATCGAATTTTGTCTGAAC 58.374 38.462 0.00 0.00 0.00 3.18
2033 2168 5.755375 GCCATAGAGATCGAATTTTGTCTGA 59.245 40.000 0.00 0.00 0.00 3.27
2035 2170 5.674525 TGCCATAGAGATCGAATTTTGTCT 58.325 37.500 0.00 0.00 0.00 3.41
2056 2193 5.973158 ACGAATTGTTGCTTAAAAACATGC 58.027 33.333 0.00 0.00 37.38 4.06
2060 2197 8.122306 AGGTTAACGAATTGTTGCTTAAAAAC 57.878 30.769 0.00 0.00 42.01 2.43
2073 2210 8.924511 ATCATCCATGATAAGGTTAACGAATT 57.075 30.769 0.00 0.00 45.17 2.17
2092 2229 7.865707 AGAAAAGCACGATAACATTATCATCC 58.134 34.615 11.26 0.31 39.55 3.51
2096 2233 5.841296 GCGAGAAAAGCACGATAACATTATC 59.159 40.000 0.00 2.08 34.62 1.75
2100 2237 3.062639 CAGCGAGAAAAGCACGATAACAT 59.937 43.478 0.00 0.00 37.01 2.71
2108 2262 2.975851 CACAAATCAGCGAGAAAAGCAC 59.024 45.455 0.00 0.00 37.01 4.40
2115 2269 2.768253 ACATCCACAAATCAGCGAGA 57.232 45.000 0.00 0.00 0.00 4.04
2134 2288 6.403866 TCAAGAAGGAAGCAGCAAAAATAA 57.596 33.333 0.00 0.00 0.00 1.40
2139 2293 3.225104 ACATCAAGAAGGAAGCAGCAAA 58.775 40.909 0.00 0.00 0.00 3.68
2143 2297 6.506500 AATGTTACATCAAGAAGGAAGCAG 57.493 37.500 0.00 0.00 0.00 4.24
2145 2299 7.414540 CCACTAATGTTACATCAAGAAGGAAGC 60.415 40.741 12.62 0.00 0.00 3.86
2146 2300 7.607991 ACCACTAATGTTACATCAAGAAGGAAG 59.392 37.037 19.42 5.03 0.00 3.46
2149 2303 7.390440 TGAACCACTAATGTTACATCAAGAAGG 59.610 37.037 12.62 14.04 0.00 3.46
2150 2304 8.322906 TGAACCACTAATGTTACATCAAGAAG 57.677 34.615 12.62 7.14 0.00 2.85
2152 2306 7.450074 ACTGAACCACTAATGTTACATCAAGA 58.550 34.615 12.62 0.00 0.00 3.02
2153 2307 7.672983 ACTGAACCACTAATGTTACATCAAG 57.327 36.000 0.00 2.37 0.00 3.02
2155 2309 9.733556 AATAACTGAACCACTAATGTTACATCA 57.266 29.630 0.00 0.00 0.00 3.07
2160 2314 9.685828 GCAAAAATAACTGAACCACTAATGTTA 57.314 29.630 0.00 0.00 0.00 2.41
2162 2316 7.151976 GGCAAAAATAACTGAACCACTAATGT 58.848 34.615 0.00 0.00 0.00 2.71
2164 2318 7.296628 TGGCAAAAATAACTGAACCACTAAT 57.703 32.000 0.00 0.00 0.00 1.73
2165 2319 6.716934 TGGCAAAAATAACTGAACCACTAA 57.283 33.333 0.00 0.00 0.00 2.24
2166 2320 6.322712 ACTTGGCAAAAATAACTGAACCACTA 59.677 34.615 0.00 0.00 0.00 2.74
2170 2324 5.234116 CACACTTGGCAAAAATAACTGAACC 59.766 40.000 0.00 0.00 0.00 3.62
2171 2325 5.234116 CCACACTTGGCAAAAATAACTGAAC 59.766 40.000 0.00 0.00 35.56 3.18
2207 2361 6.849151 TGGCTCTCAGATTACTACTACCATA 58.151 40.000 0.00 0.00 0.00 2.74
2208 2362 5.706447 TGGCTCTCAGATTACTACTACCAT 58.294 41.667 0.00 0.00 0.00 3.55
2210 2364 5.010213 CCTTGGCTCTCAGATTACTACTACC 59.990 48.000 0.00 0.00 0.00 3.18
2213 2495 4.873010 TCCTTGGCTCTCAGATTACTACT 58.127 43.478 0.00 0.00 0.00 2.57
2217 2499 2.169352 TGCTCCTTGGCTCTCAGATTAC 59.831 50.000 0.00 0.00 0.00 1.89
2226 2508 0.604578 TGCAAATTGCTCCTTGGCTC 59.395 50.000 19.34 0.00 45.31 4.70
2248 2530 0.674581 GCCCTTGGAATTTTGCAGCC 60.675 55.000 0.00 0.00 0.00 4.85
2249 2531 0.674581 GGCCCTTGGAATTTTGCAGC 60.675 55.000 0.00 0.00 0.00 5.25
2250 2532 0.978907 AGGCCCTTGGAATTTTGCAG 59.021 50.000 0.00 0.00 0.00 4.41
2323 2620 1.064017 ACAGAGGAGGCTCCAGAGTAG 60.064 57.143 33.86 18.87 39.61 2.57
2325 2622 0.614415 CACAGAGGAGGCTCCAGAGT 60.614 60.000 33.86 24.13 39.61 3.24
2326 2623 1.958902 GCACAGAGGAGGCTCCAGAG 61.959 65.000 33.86 23.51 39.61 3.35
2327 2624 1.986757 GCACAGAGGAGGCTCCAGA 60.987 63.158 33.86 0.00 39.61 3.86
2329 2626 2.203832 TGCACAGAGGAGGCTCCA 60.204 61.111 33.86 9.94 39.61 3.86
2330 2627 2.289532 ACTGCACAGAGGAGGCTCC 61.290 63.158 26.42 26.42 40.51 4.70
2331 2628 1.079266 CACTGCACAGAGGAGGCTC 60.079 63.158 5.78 5.78 40.51 4.70
2334 2631 2.745698 TGCACTGCACAGAGGAGG 59.254 61.111 4.31 0.00 40.51 4.30
2384 2684 2.869233 TTGTTGCTGCTGAAGGTTTC 57.131 45.000 0.00 0.00 0.00 2.78
2549 2854 1.153289 CTCACGGAAGGGCATGAGG 60.153 63.158 0.00 0.00 35.87 3.86
2554 2859 1.371183 CTGTTCTCACGGAAGGGCA 59.629 57.895 0.00 0.00 34.23 5.36
2643 2948 7.996066 ACACACTACTACATCTATCATCAGAGT 59.004 37.037 0.00 0.00 0.00 3.24
2671 2976 8.020819 GCATCTATCAGAACTAGTGACAGATAC 58.979 40.741 0.00 0.00 36.29 2.24
2697 3002 3.322254 AGTCTGAAGGGAACACACTACTG 59.678 47.826 0.00 0.00 0.00 2.74
2728 3033 2.079925 GATGACTTCTGGACTTGCACC 58.920 52.381 0.00 0.00 0.00 5.01
2738 3043 3.969287 TCAACCCAGAGATGACTTCTG 57.031 47.619 0.00 0.00 33.74 3.02
2805 3114 2.964464 ACTATCATCAGAGTCCAGCAGG 59.036 50.000 0.00 0.00 0.00 4.85
2813 3122 3.972638 AGGCCAATCACTATCATCAGAGT 59.027 43.478 5.01 0.00 0.00 3.24
2820 3129 3.193267 GTGCAAAAGGCCAATCACTATCA 59.807 43.478 5.01 0.00 43.89 2.15


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.